2.1. Communicating Research

It is important to have tools that allow us to communicate.

2.1.1. Blogs

blog:
noun, a regularly updated website or web page, typically one run by an individual or small group, that is written in an informal or conversational style.

Advantages:

  • encourages spontaneous posts
  • encourages small short contributions
  • chronologically ordered
  • standard software exists to set up blogs
  • online services exists to set up blogs

Disadvantages:

  • structuring data is difficult (some blog software support it)
  • not suitable for formal development of a paper
  • often lack of sophisticated track change features
  • no collaborative editing features

2.1.2. Sphinx

Sphinx (http://www.sphinx-doc.org/) is a tool that to create integrated documentation from a markup language whlie.

Advantages:

  • output formats: html, LaTeX, PDF, ePub
  • integrates well with directory structure
  • powerful markup language (reStructuredText)
  • can be hosted on github via github pages
  • can integare other renderers such as Markdown
  • automatic table of content, tebale of index
  • code documentation integration
  • search
  • written in python and using bash, so extensions and custom automation are possible

Disadvantage:

  • requires compile step
  • When using markdown github can render individual page

Others:

2.1.3. Notebooks

2.1.3.1. Jupyter

The Jupyter Notebook (http://jupyter.org/) is an open-source web application allowing users to create and share documents that contain live code, equations, visualizations and explanatory text. Use cases include data cleaning and transformation, numerical simulation, statistical modeling, machine learning.

Advantages:

  • Integrates with python
  • Recently other programming languages have been integrated
  • Allows experimenting with settings
  • Allows a form of literate programming while mixing documentation with code
  • automatically renders on github
  • comes with web service that allows hosting

Disadvantage:

  • mostly encourages short documents
  • mark up language is limited
  • editing in ASCII is complex and Web editing is prefered

2.1.3.2. Apache Zeppilin

A Web-based notebook that enables data-driven, interactive data analytics and collaborative documents with SQL, Scala and hadoop. It integrates a web-based notebook with data ingestion, data exploration, visualization, sharing and collaboration features to Hadoop and Spark.

Advantages:

  • integration to various framework
  • Web framework
  • integration with spark, hadoop

Disadvantages:

  • larger framework
  • must leverages existing deployments of spak, hadoop

2.1.4. Research Paper

To inspire you we like to start with a lecture given by Simon Peyton Jones:

2.1.4.1. Writing

  • LaTeX
  • sharelatex
  • overleaf
  • MSWord
  • OpenOffice

2.1.4.2. Bibliography management

  • JabRef
  • Endnote
  • Mendeley
  • Zotero
  • Google scholar

2.1.5. Editors

  • emacs
  • vi
  • MSWord
  • Lyx
  • various LaTeX editors
  • MacDown/Markdown editors
  • pyCharm

2.1.6. References

Collaboratories:

  • Myers JD, TC Allison, SJ Bittner, BT Didier, M Frenklach, WH Green, YL Ho, J Hewson, WS Koegler, CS Lansing, D Leahy, M Lee, R McCoy, M Minkoff, S Nijsure, G von Laszewski, D Montoya, L Oluwole, CM Pancerella, R Pinzon, W Pitz, LA Rahn, B Ruscic, KL Schuchardt, EG Stephan, A Wagner, TL Windus, and C Yang. 2005. “A Collaborative Informatics Infrastructure for Multi-scale Science.” Cluster Computing 8(4):243-253.
  • Metadata in the Collaboratory for Multi-Scale Chemical Science Carmen Pancerella, John Hewson, Wendy Koegler, David Leahy, Michael Lee, Larry Rahn, Christine Yang, James D. Myers, Brett Didier, Renata McCoy, Karen Schuchardt, Eric Stephan, Theresa Windus, Kaizar Amin, Sandra Bittner, Carina Lansing, Michael Minkoff, Sandeep Nijsure, Gregor von Laszewski, Reinhardt Pinzon, Branko Ruscic, Al Wagner, Baoshan Wang, William Pitz, Yen-Ling Ho, David Montoya, Lili Xu, Thomas C. Allison, William H. Green, Jr., Michael Frenklach http://dcpapers.dublincore.org/pubs/article/view/740/736